dwi2adc

Synopsis

Calculate ADC and/or IVIM parameters.

Usage

dwi2adc [ options ]  input output

  • input: the input image

  • output: the output ADC image

Description

The command estimates the Apparent Diffusion Coefficient (ADC) using the isotropic mono-exponential model: S(b) = S(0) * exp(-ADC * b). The value of S(0) can be optionally exported using command-line option -szero.

When using the -ivim option, the command will additionally estimate the Intra-Voxel Incoherent Motion (IVIM) parameters f and D’, i.e., the perfusion fraction and the pseudo-diffusion coefficient. IVIM assumes a bi-exponential model: S(b) = S(0) * ((1-f) * exp(-D * b) + f * exp(-D’ * b)). This command adopts a 2-stage fitting strategy, in which the ADC is first estimated based on the DWI data with b > cutoff, and the other parameters are estimated subsequently. The output consists of 4 volumes, respectively S(0), D, f, and D’.

Note that this command ignores the gradient orientation entirely. If a conventional DWI series is provided as input, all volumes will contribute equally toward the model fit irrespective of direction of diffusion sensitisation; DWI data should therefore ideally consist of isotropically-distributed gradient directions. The approach can alternatively be applied to mean DWI (trace-weighted) images.

Options

  • -szero image export image of S(0); that is, the model-estimated signal intensity in the absence of diffusion weighting

  • -ivim fraction diffusivity also estimate IVIM parameters in 2-stage fit, yielding two images encoding signal fraction and diffusivity respectively of perfusion1 component

  • -cutoff bval minimum b-value for ADC estimation in IVIM fit (default = 120 s/mm^2).

DW gradient table import options

  • -grad file Provide the diffusion-weighted gradient scheme used in the acquisition in a text file. This should be supplied as a 4xN text file with each line in the format [ X Y Z b ], where [ X Y Z ] describe the direction of the applied gradient, and b gives the b-value in units of s/mm^2. If a diffusion gradient scheme is present in the input image header, the data provided with this option will be instead used.

  • -fslgrad bvecs bvals Provide the diffusion-weighted gradient scheme used in the acquisition in FSL bvecs/bvals format files. If a diffusion gradient scheme is present in the input image header, the data provided with this option will be instead used.

Standard options

  • -info display information messages.

  • -quiet do not display information messages or progress status; alternatively, this can be achieved by setting the MRTRIX_QUIET environment variable to a non-empty string.

  • -debug display debugging messages & debug input data.

  • -force force overwrite of output files (caution: using the same file as input and output might cause unexpected behaviour).

  • -nthreads number use this number of threads in multi-threaded applications (set to 0 to disable multi-threading).

  • -config key value (multiple uses permitted) temporarily set the value of an MRtrix config file entry.

  • -help display this information page and exit.

  • -version display version information and exit.

References

Le Bihan, D.; Breton, E.; Lallemand, D.; Aubin, M.L.; Vignaud, J.; Laval-Jeantet, M. Separation of diffusion and perfusion in intravoxel incoherent motion MR imaging. Radiology, 1988, 168, 497-505.

If using -ivim option: Jalnefjord, O.; Andersson, M.; Montelius; M.; Starck, G.; Elf, A.; Johanson, V.; Svensson, J.; Ljungberg, M. Comparison of methods for estimation of the intravoxel incoherent motion (IVIM) diffusion coefficient (D) and perfusion fraction (f). Magn Reson Mater Phy, 2018, 31, 715-723.

Tournier, J.-D.; Smith, R. E.; Raffelt, D.; Tabbara, R.; Dhollander, T.; Pietsch, M.; Christiaens, D.; Jeurissen, B.; Yeh, C.-H. & Connelly, A. MRtrix3: A fast, flexible and open software framework for medical image processing and visualisation. NeuroImage, 2019, 202, 116137

Author: J-Donald Tournier (jdtournier@gmail.com) and Daan Christiaens (daan.christiaens@kuleuven.be)

Copyright: Copyright (c) 2008-2026 the MRtrix3 contributors.

This Source Code Form is subject to the terms of the Mozilla Public License, v. 2.0. If a copy of the MPL was not distributed with this file, You can obtain one at http://mozilla.org/MPL/2.0/.

Covered Software is provided under this License on an “as is” basis, without warranty of any kind, either expressed, implied, or statutory, including, without limitation, warranties that the Covered Software is free of defects, merchantable, fit for a particular purpose or non-infringing. See the Mozilla Public License v. 2.0 for more details.

For more details, see http://www.mrtrix.org/.